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add DetectLesion batch #312

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add DetectLesion batch #312

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daee136
add DetectLesion batch
mwmaclean Mar 8, 2021
bbd4e23
Apply suggestions from code review
mwmaclean Mar 8, 2021
2d31642
add 3 batches for lesion detection
mwmaclean Mar 8, 2021
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14 changes: 14 additions & 0 deletions src/batches/setBatchAbnormalitiesDetectLesion.m
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Original file line number Diff line number Diff line change
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%-----------------------------------------------------------------------
% Job saved on 08-Mar-2021 12:47:16 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3patients = '<UNDEFINED>';
matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3controls = '<UNDEFINED>';
matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3Alpha = 0.5;
matlabbatch{1}.spm.tools.ali.outliers_detection.step3tissue.step3Lambda = -4;
spmDir = spm('dir');
lesionMask = fullfile(spmDir, 'toolbox', 'ALI', 'Mask_image', 'mask_controls_vox2mm.nii');
matlabbatch{1}.spm.tools.ali.outliers_detection.step3mask_thr = 0;
matlabbatch{1}.spm.tools.ali.outliers_detection.step3binary_thr = 0.3;
matlabbatch{1}.spm.tools.ali.outliers_detection.step3binary_size = 0.8;
6 changes: 6 additions & 0 deletions src/batches/setBatchLesionOverlapMap.m
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%-----------------------------------------------------------------------
% Job saved on 08-Mar-2021 12:48:14 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.ali.lesion_overlap.lom = '<UNDEFINED>';
16 changes: 16 additions & 0 deletions src/batches/setBatchSegmentationDetectLesion.m
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%-----------------------------------------------------------------------
% Job saved on 08-Mar-2021 11:11:19 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1data = '<UNDEFINED>';
spmDir = spm('dir');
lesionPriorMap = fullfile(spmDir, 'toolbox', 'ALI', 'Priors_extraClass', 'wc4prior0.nii');
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1prior = {lesionPriorMap};
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1niti = 2;
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1thr_prob = 0.333333333333333;
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1thr_size = 0.8;
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1coregister = 1;
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1mask = {''};
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1vox = 2;
matlabbatch{1}.spm.tools.ali.unified_segmentation.step1fwhm = [8 8 8];